Can a single oxidant with two spin states masquerade as two different oxidants? A study of the sulfoxidation mechanism by cytochrome p450

Density functional calculations were performed on the sulfoxidation reaction by a model compound I (Cpd I) of cytochrome P450. By contrast to previous alkane hydroxylation studies, which exhibit a dominant low-spin (LS) pathway, the sulfoxidation follows a dominant high-spin (HS) reaction. Thus, competing hydroxylation and sulfoxidation processes as observed for instance by Jones et al. (Volz, T. J.; Rock, D. A.; Jones, J. P. J. Am. Chem. Soc. 2002, 124, 9724) are the result of a two-state reactivity scenario, whereby the hydroxylation originates from the LS pathway and the sulfoxidation from the HS pathway. In this manner, two spin states of a single oxidant (Cpd I) can be disguised as two different oxidants. The calculations rule out the possibility that a second oxidant (the ferric peroxide, Cpd 0 species) interferes in the observed results of Jones et al.     

Vibrational spectroscopic detection of H-bonded β- and γ-turns in cyclic peptides and glycopeptides

The conformation of N-glycoproteins and N-glycopeptides has been the subject of many spectroscopic studies over the past decades. However, except for some preliminary data, no detailed study on the vibrational spectroscopy of glycosylated peptides has been published until recently.

This paper reports FTIR spectroscopic properties in DMSO and TFE of the N-glycosylated cyclic peptides cyclo[Gly-Pro-Xxx(GlcNAc)-Gly-δ-Ava] 3a and 3b in comparison with data on the non-glycosylated parent peptides cyclo(Gly-Pro-Xxx-Gly-δ-Ava) 2a and 2b [a, Xxx = Asn; b, Xxx = Gln; δ-Ava = NH-(CH₂)₄-CO] and N-acetyl 2-acetamido-2-deoxy-β- -gluco pyranosylamine (GlcNAc-NHAc, 4). The assignment of amide I band frequencies to conformation is based on ROESY experiments and determination of the temperature coefficients in DMSO-d₆ solution. (For the synthesis and NMR characterization of 2a and 3a see Ref. [19].)

Cyclic peptides are expected to adopt folded (β- and/or γ-turn) conformations which may be fixed by intramolecular H-bonding(s). A comparison of the temperature coefficients of the NH protons and amide I band frequencies and intensities suggests that in DMSO there is no significant difference in the backbone conformation and H-bond system of the N-glycosylated models and their parent cyclic peptides. The common feature of the backbone conformation of models 2 and 3 is the predominance of a 1 ← 4 (C₁₀) H-bonded type II β-turn encompassing Pro-Xxx or Pro-Xxx(GlcNAc), respectively. The ROESY connectivities in the Asn(GlcNAc) model (3a) have not been found to reflect intramolecular H-bondings between the peptide and the sugar.

The unique feature of the FTIR spectra in DMSO of the cyclic models is the lack or weakness of low-frequency (< 1640 cm⁻¹) amide I component bands. In TFE the amide I region of the FTIR spectra shows an increased number of components below 1650 cm⁻¹ reflecting a mixture of open and H-bonded β- and γ-turn conformers.

Because of its destabilizing effect upon γ-turns and other weakly H-bonded structures, DMSO decreases the number of backbone conformers. DMSO also destroys side-chain-backbone H-bondings of type C₇, C₆ or C₈. Possible ‘glyco’ C₇ H-bondings in GlcNAc-NHAc (4) or in glycopeptides 3a and 3b cannot resist the effect of DMSO either.

The FTIR data in TFE of models 2–4 suggest that the acceptor amide group of strong C₇ H-bondings in peptides and glycopeptides absorbs at 1630 ± 5 cm⁻¹ and that of bifurcated H-bondings between 1600–1620 cm⁻¹.     

How does product isotope effect prove the operation of a two-state "rebound" mechanism in C-H hydroxylation by cytochrome P450?

C-H hydroxylation is a fundamental process. In Nature it is catalyzed by the enzyme cytochrome P450, in a still-debated mechanism that poses a major intellectual challenge for both experiment and theory; currently, the opinions keep swaying between the original single-state rebound mechanism, a two-oxidant mechanism (where ferric peroxide participates as a second oxidant, in addition to the primary active species, the high-valent iron-oxo species), and two-state reactivity (TSR) mechanism (where two spin states are involved). Recent product isotope effect (PIE) measurements for the trans-2-phenyl-methyl cyclopropane probe (1), led Newcomb and co-workers (Newcomb, M.; Aebisher, D.; Shen, R.; Esala, R.; Chandrasena, P.; Hollenberg, P.; Coon, M. J. J. Am. Chem. Soc. 2003, 125, 6064-6065) to rule out TSR in favor of the two-oxidant scenario, since the direction of the PIE was at odds with the one predicted from calculations on methane hydroxylation. The present report describes a density functional theoretical study of C-H hydroxylation of the Newcomb probe, 1, leading to rearranged (3) and unrearranged (2) products. Our study shows that the reaction occurs via TSR in which the high-spin pathway gives dominant rearranged products, whereas the low-spin pathway favors unrearranged products. The calculated PIE(2/3) values based on TSR are found to be in excellent agreement with the experimental data of Newcomb and co-workers. This match between experiment and theory makes a strong case that the reaction occurs via TSR mechanism.     

Two general methods for the isolation of enzyme activities by colony filter screening

We describe two general methodologies, based on filter-sandwich assays, for isolating enzymatic activities from a large repertoire of protein variants expressed in the cytoplasm of E. coli cells. The enzymes are released by the freezing and thawing of bacterial colonies grown on a porous master filter and diffuse to a second "reaction" filter that closely contacts the master filter. Reaction substrates can be immobilized either on the filter or on the enzyme itself (which is then, in turn, captured on the reaction filter). The resulting products are detected with suitable affinity reagents. We used biotin ligase as a model enzyme to assess the performance of the two methodologies. Active enzymes were released by the bacteria, locally biotinylated the immobilized target substrate peptide, and allowed the sensitive and specific detection of individual catalytically active colonies.     

Electrophilic aromatic chlorination and haloperoxidation of chloride catalyzed by polyfluorinated alcohols: a new manifestation of template catalysis

We have demonstrated that a polyfluorinated alcohol, 2,2,2-trifluoroethanol, solvent enables haloperoxidase type activity and the oxychlorination of arenes (benzene and its alkylated derivatives) without a metal catalyst. The polyfluorinated alcohol has a dual function; it catalyzes electrophilic chlorination of less reactive arenes by several orders of magnitude and oxidation of chloride at lower H+ concentrations. DFT calculations show that a complementary charge template in the transition state explains the catalysis of the electrophilic chlorination.     

Uncommon Interactions of Aliphatic Dicarboxylic Acids with Cyclodextrins

A relatively high and unexpected increase of inclusion complex stabilities could be detected in some half dissociated dicarboxylic acids (HA⁻ ions) with intramolecular H-bonding. The intermolecular hydrogen bonds between the protruding functional groups of the guest and the hydroxy groups of the host are known to enhance the stability of the cyclodextrin (CD) inclusion complexes. The enhanced inclusion of HA⁻ species is promoted, not by the intermolecular but by the intramolecular H-bond indirectly, resulting in a compact shape of the guest with more favourable space filling.